New York (CNN) -- Coalition forces have scored gains on the Afghan battlefield. Taliban leaders are on the run in neighboring Pakistan. But there's no sign of political progress in Afghanistan, says analyst Fareed Zakaria.

He said Afghan President Hamid Karzai's assertion of control this week over a watchdog group that seeks to ensure fair elections is "just one more reminder that we have a very difficult alliance with Karzai."

Zakaria said, "You notice that even though the coalition gave Karzai enormous control over the military operations in Marjah, he has yet to publicly endorse them. He has twice publicly criticized them for civilian casualties without pointing out that the Taliban makes conscious use of civilians as human shields. So overall his recent actions have all reminded us that he is playing political games rather than providing real leadership."

NATO-led and Afghan troops have gained ground in a major offensive in the southern province of Helmand, but also have stirred protests about civilian casualties that are believed to have claimed more than 50 lives in two weeks. U.S. Gen. Stanley McChrystal apologized for an airstrike in which 27 civilians were killed.

Zakaria, author and host of CNN's "Fareed Zakaria GPS," spoke to CNN on Thursday. Here is an edited transcript:

CNN: What's your overall assessment of whether NATO is making progress in Afghanistan?

Fareed Zakaria: All recent signs have been good. As I expected, clearly the American armed forces are doing very well in the military realm. Clearly having more troops and having them engaged is translating into military success on the ground. It does remain to be seen whether these Taliban forces are away so that they can then reconstitute themselves and come back or whether they are permanently defeated.

We still don't know how the politics of this is going to play out. Gen. McChrystal said that after they clear the area of the Taliban, they have "government in a box" that they were going to roll out in all these areas. I think that's a very unfortunate phrase because governments don't exist in boxes. It's not like we have any machine called government to put in place.

The problem has always been in Afghanistan getting a good government in place, a legitimate, responsive and efficient government. So I hope that this time it will succeed. But that has been the problem so far, that Afghan government in or out of the box has been weak, indecisive and corrupt.

CNN: What do you think of the action of President Karzai in seizing control of the election process?

Zakaria: It's not what he had promised to do, and it's disappointing. ... There is no alternative to Karzai, so I'm not suggesting replacing him in any fashion even if we could, but it limits the effectiveness of all of these operations.

CNN: What is his strategy?

Zakaria: His strategy is to co-opt allies who will help keep him in power, which means trying to ally with warlords here and there, pandering to public opinion here and there, while not putting a focus on the long-term welfare of Afghanistan and making sure this mission succeeds in stabilizing it.

CNN: On this question of the most recent incidents of civilian casualties, Gen. McChrystal had promised that it was going to be a high priority to prevent these deaths. Why haven't they been prevented?

Zakaria: For two reasons. War is a very complicated, uncertain activity in which you don't have perfect information, you don't have perfect knowledge, so there is going to have to be collateral damage. That is one of the reasons why you should always be careful about initiating war. The second reason is that the Taliban is very deliberately and consciously using human shields, which of course exacerbates the problem because if you try to strike at them, you inevitably are going to strike at some of the civilians they've surrounded themselves with.

CNN: Do you think the U.S. is making any progress in improving its ability to target?

Zakaria: American tactics, compared to 20 to 30 years ago, have gotten much more precise. The targeting is better, the intelligence is better, but frankly you're never going to be 100 percent effective. The Army is right the vast majority of times. The few incidents where there are civilian casualties always make the news. It's a very difficult part of modern warfare for a democracy.

CNN: How important is this in the larger question of winning the hearts and minds of the Afghan people?

Zakaria: It's important, but I think it's more important to get the politics right, to get in place an Afghan government that both understands these realities, and is seen as legitimate by its people, and is supporting the aspirations of providing services to the Afghan people. If that happens, people will understand that this is a very sad but temporary problem, but that they are on the path to getting control over their lives. If it seems to be happening in the absence of that progress, naturally these casualties take on a life of their own, heighten the sense of anti-Americanism and the desire to throw the foreigners out.

CNN: We've seen a number of captures of ranking Taliban officials by the Pakistanis. Do you think that's a turning point?

Zakaria: It's certainly very positive news. It has been true now for almost nine years -- ever since 9/11 -- that the U.S. has been trying to get the Pakistani military to focus on the key leadership of the Taliban, all of whom are in Pakistan, and they have been very reluctant to do so. But it does appear that there has been a change.

It's worth giving credit to the Obama administration, which has worked very seriously on the Pakistan end of this problem and to the Pakistani military, which seems to have gotten out of its myopia of exclusively focusing on India and seems to realize there's a broader threat.

All that said, from my sources, it's still unclear whether this is a general transformation of the Pakistani military or whether this is a set of concessions they've made to Washington because the Obama administration has been very insistent on this issue. If it is the latter, while we may see a few more, we will not see the wholesale routing of the Taliban in Pakistan which we've been hoping for.

CNN: What else needs to be done?

Zakaria: The crucial next step which needs to take place is the splitting of the Taliban. The Taliban in terms of the number of troops is quite large, and some of these groups seem to be Pashtun nationalists. Pashtuns are an ethnic group that make up 50 percent of Afghanistan. It's an ethnic group that feels somewhat disempowered by the changes which have taken place in last decade.

If we can get some percentage of those disaffected Pashtuns to stop supporting the Taliban and to start supporting the Afghan government, that would cripple the Taliban because it would mean it could no longer be able to claim it can represent the Pashtun resistance to the Karzai government.

Karzai is a Pashtun himself, but a lot of Pashtuns feel that he has presided over a government dominated by non-Pashtuns, particularly in the military.

But that's the key -- and it was the key in Iraq: Giving those who feel disempowered or feel they were being persecuted under the new regime, giving them some reason to think that isn't the case so you can bring them back into the tent.